Line data    Source code

       1             : /* 
       2             : * Copyright (C) 2020-2024 MEmilio
       3             : *
       4             : * Authors: Lena Ploetzke
       5             : *
       6             : * Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
       7             : *
       8             : * Licensed under the Apache License, Version 2.0 (the "License");
       9             : * you may not use this file except in compliance with the License.
      10             : * You may obtain a copy of the License at
      11             : *
      12             : *     http://www.apache.org/licenses/LICENSE-2.0
      13             : *
      14             : * Unless required by applicable law or agreed to in writing, software
      15             : * distributed under the License is distributed on an "AS IS" BASIS,
      16             : * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
      17             : * See the License for the specific language governing permissions and
      18             : * limitations under the License.
      19             : */
      20             : 
      21             : #ifndef IDE_SEIR_PARAMS_H
      22             : #define IDE_SEIR_PARAMS_H
      23             : 
      24             : #include "memilio/math/eigen.h"
      25             : #include "memilio/epidemiology/uncertain_matrix.h"
      26             : #include "memilio/utils/parameter_set.h"
      27             : 
      28             : namespace mio
      29             : {
      30             : namespace iseir
      31             : {
      32             : /****************************************************
      33             : * define some parameters used in the IDE SEIR model *
      34             : *****************************************************/
      35             : 
      36             : /**
      37             :  * @brief The time of latency used in the IDE SEIR model.
      38             :  * 
      39             :  * Latency time is the average time from infection to the onset of infectivity used in the model.
      40             :  * Latency time is measured in days.
      41             :  */
      42             : struct LatencyTime {
      43             :     using Type = double;
      44           2 :     static constexpr Type get_default()
      45             :     {
      46           2 :         return 3.3;
      47             :     }
      48             : };
      49             : 
      50             : /**
      51             :  * @brief The infectious time used in the IDE SEIR model.
      52             :  * 
      53             :  * Infectious time is the average time from onset of infectivity to recovery used in the model.
      54             :  * Infectious time is measured in days.
      55             :  */
      56             : struct InfectiousTime {
      57             :     using Type = double;
      58           2 :     static constexpr Type get_default()
      59             :     {
      60           2 :         return 8.2;
      61             :     }
      62             : };
      63             : 
      64             : /**
      65             :  * @brief The risk of transmission in the event of a contact used in the IDE SEIR model.
      66             :  * 
      67             :  * The transmission risk is the average risk to get infected in the event of a contact, 
      68             :  * given that the contact takes place between a susceptible and an infected person.
      69             :  */
      70             : struct TransmissionRisk {
      71             :     using Type = double;
      72           2 :     static constexpr Type get_default()
      73             :     {
      74           2 :         return 0.1;
      75             :     }
      76             : };
      77             : 
      78             : /**
      79             :  * @brief The contact frequency is modeled using an UncertainContactMatrix.
      80             :  * 
      81             :  * The contact frequency is the average number of contact of an individual per day.
      82             :  * We use the type UncertainContactMatrix, because of the Randomness in this variable.
      83             :  * Via this parameter, dampings can be included to simulate non-pharmaceutical interventions.
      84             :  */
      85             : template <typename FP = double>
      86             : struct ContactFrequency {
      87             :     using Type = UncertainContactMatrix<FP>;
      88           2 :     static Type get_default()
      89             :     {
      90           2 :         ContactMatrixGroup contact_matrix = ContactMatrixGroup(1, 1);
      91           2 :         contact_matrix[0]                 = mio::ContactMatrix(Eigen::MatrixXd::Constant(1, 1, 10.));
      92           4 :         return Type(contact_matrix);
      93           2 :     }
      94             : };
      95             : 
      96             : // Define Parameterset for IDE SEIR model.
      97             : template <typename FP = double>
      98             : using ParametersBase = ParameterSet<TransmissionRisk, LatencyTime, InfectiousTime, ContactFrequency<FP>>;
      99             : 
     100             : } // namespace iseir
     101             : } // namespace mio
     102             : 
     103             : #endif